For cryo em facilities

Scipion will process your acquired images on the fly and will provide feedback to help you make decisions while the microscope is collecting data.


Multiple options are available to process your data on the fly such as running in batches or multi-GPU jobs handling. Get the most out of your microscope by analyzing results as quick as possible!

Facilities documentation


Most popular image processing packages like Relion 3, motioncor2, ctffind4, crYOLO, Xmipp, and many more are now integrated. And tomography packages are about to be published as plugins.

See all integrated packages


Most of the steps in SPA analysis in Scipion have several options and is up to YOU to choose them. All this without the need of any programming skills. You can even use several different methods and then apply consensus tools.

See methods by steps.


Designed to integrate and be integrated. All its functionality can be accessed from any python code (in case you need it) and from version 2.0 it is a plugin-framework. So, you will have what is integrated today, and what the "em developers community" will integrate tomorrow.

See developers information.


You can automate all this only with a few clicks, so Scipion will not bother you unless something goes wrong or you want to have a look at the results


You can apply consensus methods to compare alignments, CTFs and pickings to prune the images providing your users with a "clean" dataset to start the reconstruction.

Live HTML acquisition report

You can choose to generate a detailed summary report (in HTML) ready to sync to any public HTTP server, so your external users can follow the data collection progress.

Sample report

Which facilities are using Scipion?